The main group consists of indices into the extended group, you can't have modes in main that are not in extended. Let's take a look at the configuration array:
const uint8_t EEMEM eeprom[64] =
{ 0x00, 0xFF, 0xFF, 0x00,
0x00, 0x00, 0x00, 0x00,
0x00, 0x00, 0x00,
// initial mode programming, indices to mode lines in the following array
0x03, 0x06, 0x08, 0x00, 0x00,
// mode configuration starts here. Format is:
// offset in mode_func_arr, func data1, func data2, func data3
MODE_LVL001, // 0x00
MODE_LVL002, // 0x01
MODE_LVL004, // 0x02
MODE_LVL008, // 0x03
MODE_LVL016, // 0x04
MODE_LVL032, // 0x05
MODE_LVL064, // 0x06
MODE_LVL128, // 0x07
MODE_LVL255, // 0x08
MODE_STROBE, // 0x09
MODE_POLICE, // 0x0A
MODE_BEACON // 0x0B
};
The main group is configured by the line:
// initial mode programming, indices to mode lines in the following array
0x03, 0x06, 0x08, 0x00, 0x00,
These are offsets into the extended group. The first mode is at offset 0x03 (MODE_LVL008), the second is at offset 0x06 (MODE_LVL64) and the third is at offset 0x08 (MODE_LVL255). The fourth and fifth slot are not used because NUM_MODES is set to 3. If you re-arrange the modes in the extended group, you will have to adjust these indices.